Sorry if I hijacked this thread a little towards the science, but this is what I love about this forum, there is so much knowledge to share with others.
Those were good questions. Sometimes, it's important to have clarity on some basic points to understand something more complex.
Their bodies deal with physical irritants by secreting nacre to protect the delicate tissues from damage, but that does not mean they experience pain-- or happiness. I would think one needs a brain for that.
Shellfish have reflexes, but not pain as we know it.
The first part of your point is worth commenting to the topic. A point often missed, the opposite is also true. Shellfish have the ability errode shell with acids every bit as easily as the ability to build shell with bases. No more is this apparent than when a mollusk repairs a broken shell. So complexed are the epithelial cells, they are able to perform one function or the other, in adjacent cells. It's particularily ongoing in scallops normally, which gives rise to the commonly "dimpled" textures in both pearls and shells. Mussel shells are like razor blades when cracked. Attempting to mineralize an "irritant" such as this, would likely exacerbate the injury because of the close proximity of the cells, whereas backing off a bit, then applying acid will wear down the sharp surface.
Ocean salinity is not constant. In fact, (especially in the temperate zones) it's up and down the scale, sometimes with extremes with rains and floods. All living things need calcium and if they cannot get it from food they take it from shells or bones. Even at best, it's always a balance of a two way street.
Jeremy made an very important point from a commercial standpoint, while from a biological position, the ideal nucleus is one that behaves as biologicals behave. One might argue that plastic gets used for mabes (extrapallial pearls) all the time and opals and mud have been successfully used as nuclei for gonadal pearls, but they are far from ideal.
I suppose a matrix of calcium carbonate, aragonite... possibly vaterite might do well to form beads of correct hardness and surface tension, but then it becomes an issue of viability.
Last report is there remains a glut on American mussel shells and the need to look to a synthetic alternative isn't all that important at this time.